July 27, 2008
Announcement: BC Net Workshop
Tis the season for networks workshops, it seems. Here's another announcement I recently received, this time for a workshop in Barcelona. Although the keynote-speaker lineup looks pretty good, and the organizers have done a lot of interesting work over the years, I will probably have to skip this event as I'm running a workshop on Networks and Inference at SFI only a few days before. If any of my dear readers go, I'd love to get a summary afterward.
BC Net Workshop: Trends and perspectives in complex networks
Description: Ten years have elapsed since the publication of the celebrated paper by Watts and Strogatz on small-world networks. During this decade, the development of foundational aspects and methodologies set the grounds of complex network science, an interdisciplinary research area connecting Statistical Physics, Biology, Information Technology, Sociology, Economy, and others. Time has come to ask what have been the major contributions of this emerging field to prospect its future in perspective. We believe network science is now mature enough to start developing problem-solving ability and engineering and predictive power.
The spirit of this workshop is to stimulate researchers in complex networks and related areas to find new perspectives, trends, and applications that guarantee this headway. To this end, internationally recognized specialists will be invited to explain their current investigations and to discuss the expected progress of their research within the context of the field. The workshop will present as well selected contributions compliant with its purpose. An open colloquium session will also be organized where keynote speakers, participants, and committee members will have the opportunity to debate all together on the present situation of complex networks science and its outlook.
It's hard to top the explanation that NASA's Astro Photo of the Day page gave to this video, so I'll just quote it here:
What are these humans doing? Dancing. Many humans on Earth exhibit periods of happiness, and one method of displaying happiness is dancing. Happiness and dancing transcend political boundaries and occur in practically every human society. Above, Matt Harding traveled through many nations on Earth, started dancing, and filmed the result. The video is perhaps a dramatic example that humans from all over planet Earth feel a common bond as part of a single species. Happiness is frequently contagious -- few people are able to watch the above video without smiling.
July 21, 2008
Evolution and Distribution of Species Body Size
One of the most conspicuous and most important characteristics of any organism is its size : the size basically determines the type of physics it faces, i.e., what kind of world it has to live in. For instance, bacteria live in a very different world from insects, and insects live in a very different world from most mammals. In a bacterium's world, nanometers and micrometers are typical scales and some quantum effects are significant enough to drive some behaviors, but larger-scale effects like surface tension and gravity have a much more indirect effect. For most insects, typical scales are millimeter and centimeters, where quantum effects are negligible, but the surface tension of water matters tremendously. Similarly, for most mammals , a typical scale is more like a meter, and surface tension isn't as important as gravity and supporting your own body weight.
And yet despite these vast differences in the basic physical world that different types of species encounter, the distribution of body sizes within a taxonomic group, that is, the relative number of small, medium and large species, seems basically the same regardless of whether we're talking about insects, fish, birds or mammals: a few species in a given group are very small (about 2 grams for mammals), most species are slightly larger (between 20 and 80 grams for mammals), but some species are much (much!) larger (like elephants, which weigh over 1,000,000 times more than the smallest mammal). The ubiquity of this distribution has intrigued biologists since they first began to assemble large data sets in the second-half of the 20th century.
Many ideas have been suggested about what might cause this particular, highly asymmetric distribution, and they basically group into two kinds of theories: optimal body-size and diffusion. My interest in answering this question began last summer, partly as a result of some conversations with Alison Boyer in another context. Happily, the results of this project were published in Science last week  and basically show that the diffusion explanation is, when fossil data is taken in account, really quite good. (I won't go into the optimal body-size theories here; suffice to say that it's not as popular a theory as the diffusion explanation.) At its most basic, the paper shows that, while there are many factors that influence whether a species gets bigger or smaller as it evolves over long periods of time, their combined influence can be modeled as a simple random walk . For mammals, the diffusion process is, surprisingly I think, not completely agnostic about the current size of a species. That is, although a species experiences many different pressures to get bigger or smaller, the combined pressure typically favors getting a little bigger (but not always). The result of this slight bias toward larger sizes is that descendent species are, on average, 4% larger than their ancestors.
But, the diffusion itself is not completely free , and its limitations turn out to be what cause the relative frequencies of large and small species to be so asymmetric. On the low end of the scale, there are unique problems that small species face that make it hard to be small. For instance, in 1948, O. P. Pearson published a one-page paper in Science reporting work where he, basically, stuck a bunch of small mammals in an incubator and measured their oxygen (O2) consumption. What he discovered is that O2 consumption (a proxy for metabolic rate) goes through the roof near 2 grams, suggesting that (adult) mammals smaller than this size might not be able to find enough high-energy food to survive, and that, effectively, 2 grams is the lower limit on mammalian size . On the upper end, there is an increasingly dire long-term risk of become extinct the bigger a species is. Empirical evidence, both from modern species experiencing stress (mainly from human-related sources) as well as fossil data, suggests that extinction seems to kill off larger species more quickly than smaller species, with the net result being that it's hard to be big, too.
Together, this hard lower-limit and soft upper-limit on the diffusion of species sizes shape distribution of species in an asymmetric way and create the distribution of species sizes we see today . To test this hypothesis in a strong way, we first estimated the details of the diffusion model (such as the location of the lower limit and the strength of the diffusion process) from fossil data on about 1100 extinct mammals from North America that ranged from 100 million years ago to about 50,000 years ago. We then simulated about 60 million years of mammalian evolution (since dinosaurs died out), and discovered that the model produced almost exactly the size distribution of currently living mammals. Also, when we removed any piece of the model, the agreement with the data became significantly worse, suggesting that we really do need all three pieces: the lower limit, the size-dependent extinction risk, and the diffusion process. The only thing that wasn't necessary was, surprisingly, the bias toward slightly larger species in the diffusion itself , which I think most people thought was necessary to produce really big species like elephants.
Although this paper answers several questions about why the distribution of species body size is the way it is, there are several questions left unanswered, which I might try to work on a little in the future. In general, one exciting thing is that this model offers some possibilities for connecting macroevolutionary patterns, such as the distribution of species body sizes over evolutionary time, with ecological processes, such as the ones that make larger species become extinct more quickly than small species, in a relatively compact way. That gives me some comfort, since I'm sympathetic to the idea that there are reasons we see such distinct patterns in the aggregate behavior of biology, and that it's possible to understand something about them without having to understand the specific details of every species and every environment.
 An organism's size is closely related, but not exactly the same as its mass. For mammals, their density is very close to that of water, but plants and insects, for instance, can be less or more dense than water, depending on the extent of specialized structures.
 The typical mammal species weights about 40 grams, which is the size of the Pacific rat. The smallest known mammal species are the Etruscan shrew and the bumblebee bat, both of whom weight about 2 grams. Surprisingly, there are several insect species that are larger, such as the titan beetle which is known to weigh roughly 35 grams as an adult. Amazingly, there are some other species that are larger still. Some evidence suggests that it is the oxygen concentration in the atmosphere that mainly limits the maximum size of insects. So, about 300 million years ago, when the atmospheric oxygen concentrations were much higher, it should be no surprise that the largest insects were also much larger.
 A. Clauset and D. H. Erwin, "The evolution and distribution of species body size." Science 321, 399 - 401 (2008).
 Actually, in the case of body size variation, the random walk is multiplicative meaning that changes to species size are more like the way your bank balance changes, in which size increases or decreases by some percentage, and less like the way a drunkard wanders, in which size changes by increasing or decreasing by roughly constant amounts (e.g., the length of the drunkard's stride).
 If it were a completely free process, with no limits on the upper or lower ends, then the distribution would be a lot more symmetric than it is, with just as many tiny species as enormous species. For instance, with mammals, an elephant weights about 10 million grams, and there are a couple of species in this range of size. A completely free process would thus also generate a species that weighed about 0.000001 grams. So, the fact that the real distribution is asymmetric implies that some constraints much exist.
 The point about adult size is actually an important one, because all mammals (indeed, all species) begin life much smaller. My understanding is that we don't really understand very well the differences between adult and juvenile metabolism, how juveniles get away with having a much higher metabolism than their adult counterparts, or what really changes metabolically as a juvenile becomes an adult. If we did, then I suspect we would have a better theoretical explanation for why adult metabolic rate seems to diverge at the lower end of the size spectrum.
 Actually, we see fewer large species today than we might have 10,000 - 50,000 years ago, because an increasing number of them have died out. The most recent population collapses are certainly due to human activities such as hunting, habitat destruction, pollution, etc., but even 10,000 years ago, there's some evidence that the disappearnace of the largest species was due to human activities. To control for this anthropic influence, we actually used data on mammal species from about 50,000 years ago as our proxy for the "natural" state.
July 15, 2008
Announcement: ICDM Workshop on Analysis of Dynamic Networks
Since I'm pretty sure that part of the future of research on complex networks lays in understanding how networks evolve over time, this workshop seems quite relevant. Judging by the associated conference and the organizers, this workshop will probably focus on algorithmic techniques for analyzing large amounts of network data.
December 19, 2008 at the IEEE Conference on Data Mining (ICDM) in Pisa, Italy
Description: The goal of the Analysis of Dynamic Networks (ADN) workshop is to bring together research that addresses explicitly the dynamic nature of networks in the context of analysis of social, electronic, biological and other networks. We aim to further the development of a computational framework in which one can model, discover and analyze complex interaction systems as they form and evolve.
We invite contributions presenting new computational methods for analysis of dynamic interaction networks, new models of dynamic behavior of networks, or applications of dynamic network analysis in various contexts. Papers presenting new methods should provide experimental or empirical evidence of the performance of the new methods.
In this context, submission topics can include, but are not limited to:
- Modeling dynamic behavior of networks
- Network structure prediction
- Analysis of spreading processes in networks
- Community structure inference
- Search and routing in dynamic networks
- Identification of critical nodes
- Comparison of dynamic networks
- Visualization of dynamic networks
Other topics within the subject area are welcome. Note, that all submitted papers should demonstrate the relevance to the topic of dynamic networks. If unsure whether your paper fits the session theme, please contact one of the co-chairs.
July 09, 2008
Announcement: DIMACS Workshop on Network Models of Biological and Social Contagion
This workshop looks pretty interesting, and that's not because it's being organized by my friends. Comfortably, the topics align with several of what I think are the "future" of network science (tip to Jake).
Update 18 July 2008: Having just received an invitation to speak from the organizers, I think it's likely that I'll be attending. In addition to learning about new science at DIMACS, it'll be a great opportunity to also visit some friends and colleagues in New York City.
November 3 - 4, 2008 at DIMACS, Rutgers
Description: The spread of infectious diseases and the flow of ideas and information through populations fundamentally depend on the complex structure of the underlying network of interactions between individuals. Disease ecologists and sociologists have historically studied the dynamics of contagion using models that assume very simple population structures. Recently, however, network modeling has revolutionized both fields by enabling the rigorous exploration of the relationship between complex individual-level behavior and the higher-level emergence of outbreaks. The field draws on advanced statistical tools for inferring network structure from often limited data, data-driven algorithms for generating realistic network structures, and mathematical approximations for predicting transmission dynamics that draw from the methods of percolation theory and other fields within statistical physics.
While network models are more complex than their mass-action predecessors, they are remarkably tractable, often reducing to low-dimensional descriptions and allowing straightforward calculations of the dynamics of contagion. The fields of infectious disease epidemiology and sociology are simultaneously experiencing an explosion of computationally-intensive agent-based simulation models, that allow much higher-resolution representations of populations but often preclude comprehensive analysis. Selecting among the diversity of modeling approaches is non-trivial, and may be highly dependent on the system and the questions.
This workshop will focus on network models for biological and social contagion, and how they compare to alternative approaches. It will address the challenges of inferring network structure from sociological and/or epidemiological data, understanding the emergence of such network structure from simple individual-level behavior, and predicting the dynamics of contagion from simple characterizations of the underlying network.
- Inferring network structure from data
- Generative models of social and epidemiological networks
- Modeling the dynamics of biological and social contagion on networks
- Modeling feedback from contagion dynamics to network structure
- Model selection -- choosing the right level of complexity
July 03, 2008
A quick trip to China
Today I leave for Beijing China, where I'll be giving a few lectures as part of the 2008 China / SFI Complex Systems Summer School (CSSS). It should be an interesting experience for many reasons. I'm also looking forward to seeing a few of the touristy sights, such as Tiananmen Square, the Forbidden City, the Summer Palace, the Great Wall, and the new Olympic pavilion.
Update 18 July 2008: My lecture notes are now online on the Beijing CSSS wiki here. I gave two lectures on the basics of complex networks, and one lecture on power laws in empirical data.
Update 18 July 2008: It's hard to summarize the overall impression I had of Beijing in particular, and China in general; but, I'll try. Beijing is a city bustling with life. A wide zone of feverish development and heavy air pollution (but not trash - the city was surprisingly clean except for the dingy-ness the heavy smog left on all surfaces), it's also a study of different aspects of Chinese society modernizing at different rates. Beijing is knocking down the traditional hutongs (the traditional, one or two story residential and light commercial buildings that used to blanket the Beijing landscape), often over the protests of their residents but not always, to build the skyscrapers and apartment towers of a modern, dense city. The exchange rate, and government policies, made taxis very affordable, and while riding around, I spotted both the ugly concrete towers as well as the beautiful glass and steel constructions that would look at home in Zurich or New York. There were also several buildings most notable for their striking architecture ; most of these are for the Olympics, but not all of them - some were simply upscale residential, office or hotel buildings.
It wasn't clear to me that the regular Beijinger was excited about the upcoming Olympics (starting in just three weeks), but certainly the government is. Olympic decorations and advertisements were everywhere, and the mascots (the five Fuwa) were ubiquitous. And yet, when I walked through the Olympic pavilion area, there was obviously still a tremendous amount of work left to be done. I'm told that Athens was even further behind schedule for the 2000 Olympics, so maybe it will all work out. The Olympic areas were also some of the places where the military presence was the strongest, with lots of fences and guards. Oddly, there was even a military installation (with tanks) just to the south of one of the sports complexes.
My favorite picture of the 300 odd that I took (many of which are now on my Flickr photostream) while bouncing around the city is of a man on a traditional bicycle yakking away on his cell phone. A lot of people still ride bicycles, but apparently cars are increasingly popular. Owning one is now a status symbol, as it used to be in America , and many Beijingers are taking to it with enthusiasm, even though the traffic is already terrible. I'm told that some American car makers are doing very well in the growing Chinese market, to the point that their recent growth was driven almost entirely by Chinese sales . Designer goods that are fashionable in the West are also popular in Beijing, but surprisingly, they don't cost any less. So, a well-to-do Beijinger will spend $300 on a Coach purse even though it costs 2000 yuan, enough to buy a nice dinner every night for a month. Another interesting observation about Beijing is that most of the commercial stores (not the small businesses, but rather the larger enterprises) were overstaffed. At several restaurants, I noticed at least three or four times as many waitstaff as were necessary to actually run the place. I'd like to think this is indicative of the larger problem China faces with a burgeoning labor force, but who knows.
 Coincidentally, the NY Times put up an interactive graphic that discusses five of these, mostly built in prep for the Olympics. I saw all of them, from a distance, except for "Big Shorts" (the new national television building). The New Yorker also has a short piece about these buildings, and the Beijing skyline in general. I highly recommend both of these.
 Owning a car in the US is no longer enough to show everyone else that you're rich and know it. Now you have to drive a big car, preferably something like a Hummer or an FJ.
 Someone told me that Buick, of all brands, is very popular in China because it was the brand that the last Emperor favored.